Alignments for a candidate for hutH in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutH in Burkholderia phytofirmans PsJN

Align Histidine ammonia-lyase (EC 4.3.1.3) (characterized)
to candidate BPHYT_RS07555 BPHYT_RS07555 histidine ammonia-lyase

Query= reanno::BFirm:BPHYT_RS07555
         (506 letters)



>FitnessBrowser__BFirm:BPHYT_RS07555
          Length = 506

 Score =  977 bits (2525), Expect = 0.0
 Identities = 506/506 (100%), Positives = 506/506 (100%)

Query: 1   MTLKPGYLTLPQLRQIAREHVALQLDPASHAAIDACAQAVADIAAKGEPAYGINTGFGRL 60
           MTLKPGYLTLPQLRQIAREHVALQLDPASHAAIDACAQAVADIAAKGEPAYGINTGFGRL
Sbjct: 1   MTLKPGYLTLPQLRQIAREHVALQLDPASHAAIDACAQAVADIAAKGEPAYGINTGFGRL 60

Query: 61  ASTHIPHDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEAL 120
           ASTHIPHDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEAL
Sbjct: 61  ASTHIPHDQLELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEAL 120

Query: 121 ITLYNADVLPVIPVKGSVGASGDLAPLAHMSATLLGVGEVFAKGERMPATEGLALVGLKP 180
           ITLYNADVLPVIPVKGSVGASGDLAPLAHMSATLLGVGEVFAKGERMPATEGLALVGLKP
Sbjct: 121 ITLYNADVLPVIPVKGSVGASGDLAPLAHMSATLLGVGEVFAKGERMPATEGLALVGLKP 180

Query: 181 LTLQAKEGLALLNGTQASTALALYNMFAIEDLYRTALVSGALSVDAAMGSVKPFDARIHE 240
           LTLQAKEGLALLNGTQASTALALYNMFAIEDLYRTALVSGALSVDAAMGSVKPFDARIHE
Sbjct: 181 LTLQAKEGLALLNGTQASTALALYNMFAIEDLYRTALVSGALSVDAAMGSVKPFDARIHE 240

Query: 241 LRGHQGQIDAAGAYRSLLQGSGINVSHADCDKVQDPYSLRCQPQVMGACLDQMRHAANVL 300
           LRGHQGQIDAAGAYRSLLQGSGINVSHADCDKVQDPYSLRCQPQVMGACLDQMRHAANVL
Sbjct: 241 LRGHQGQIDAAGAYRSLLQGSGINVSHADCDKVQDPYSLRCQPQVMGACLDQMRHAANVL 300

Query: 301 LLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAERRIALLIDAT 360
           LLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAERRIALLIDAT
Sbjct: 301 LLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAERRIALLIDAT 360

Query: 361 LSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATFA 420
           LSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATFA
Sbjct: 361 LSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATFA 420

Query: 421 ARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMDAVRKDVAHYELDHYFAP 480
           ARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMDAVRKDVAHYELDHYFAP
Sbjct: 421 ARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMDAVRKDVAHYELDHYFAP 480

Query: 481 DIAAVTRLVQDGTIAKLSPLSFASEQ 506
           DIAAVTRLVQDGTIAKLSPLSFASEQ
Sbjct: 481 DIAAVTRLVQDGTIAKLSPLSFASEQ 506


Lambda     K      H
   0.318    0.133    0.374 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 972
Number of extensions: 31
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate BPHYT_RS07555 BPHYT_RS07555 (histidine ammonia-lyase)
to HMM TIGR01225 (hutH: histidine ammonia-lyase (EC 4.3.1.3))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01225.hmm
# target sequence database:        /tmp/gapView.17750.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01225  [M=506]
Accession:   TIGR01225
Description: hutH: histidine ammonia-lyase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.1e-216  705.2   7.0   2.5e-216  704.9   7.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07555  BPHYT_RS07555 histidine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07555  BPHYT_RS07555 histidine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  704.9   7.0  2.5e-216  2.5e-216       1     497 [.       1     497 [.       1     504 [. 0.99

  Alignments for each domain:
  == domain 1  score: 704.9 bits;  conditional E-value: 2.5e-216
                                TIGR01225   1 vvldgesltledleavarekarvelsaaaeeavaksravieeivaedktvYGvntGFGklasvkidkedl 70 
                                              ++l+++ ltl +l+++are+  ++l+ a+++a+++ ++++++i+a+ ++ YG+ntGFG+las++i +++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555   1 MTLKPGYLTLPQLRQIAREHVALQLDPASHAAIDACAQAVADIAAKGEPAYGINTGFGRLASTHIPHDQL 70 
                                              689999**************************************************************** PP

                                TIGR01225  71 aeLqrnlvrsHaaGvGepleeevvRallvlrlnslakGysgvraevlellvallnaevlPvvpekGsvGa 140
                                              + Lqrnlv+sHa+GvGep+++ vvR+l++l+l sl +G+sg+r+ev+e+l+ l na+vlPv+p kGsvGa
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555  71 ELLQRNLVLSHAVGVGEPMSRPVVRLLIALKLSSLGRGHSGIRREVMEALITLYNADVLPVIPVKGSVGA 140
                                              ********************************************************************** PP

                                TIGR01225 141 sGDLAPLahlalvliGeGeaefegevmdaaeaLaaaglePvtlkakEGlALinGtqlmtalavlalvdae 210
                                              sGDLAPLah++++l+G Ge++ +ge+m+a+e La  gl+P+tl+akEGlAL+nGtq++tala+  ++ +e
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555 141 SGDLAPLAHMSATLLGVGEVFAKGERMPATEGLALVGLKPLTLQAKEGLALLNGTQASTALALYNMFAIE 210
                                              ********************************************************************** PP

                                TIGR01225 211 kllesadiaaalsleallgtskafdpdihevrphrgqiavaarlrellagseiaeshkdedrvqDaYslR 280
                                              +l+++a +++als++a++g+ k+fd++ihe+r+h+gqi+ a + r+ll+gs+i  sh d+d+vqD+YslR
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555 211 DLYRTALVSGALSVDAAMGSVKPFDARIHELRGHQGQIDAAGAYRSLLQGSGINVSHADCDKVQDPYSLR 280
                                              ********************************************************************** PP

                                TIGR01225 281 ciPqvhGavldtldqvkevlaiElnsatDnPlvfadegevvsgGnFHgepvAlaldflaiaiaelgaise 350
                                              c+Pqv+Ga+ld+++++++vl  E+n+++DnPl+f+d+gev sgGnFH+epvA+a+d+la+a+ae+ga++e
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555 281 CQPQVMGACLDQMRHAANVLLLEANAVSDNPLIFPDTGEVLSGGNFHAEPVAFAADNLALAAAEIGALAE 350
                                              ********************************************************************** PP

                                TIGR01225 351 RRierlldpalseLppFLaedsGlnsGlmiaqytaAaLvsenkaLahPasvDsiptsanqEDHvsmgaaa 420
                                              RRi++l+d +ls+LppFL+ d+G+nsG+mia++taAaL+senk+LahPasvDs+ptsanqEDHvsm++ a
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555 351 RRIALLIDATLSGLPPFLVRDGGVNSGFMIAHVTAAALASENKTLAHPASVDSLPTSANQEDHVSMATFA 420
                                              ********************************************************************** PP

                                TIGR01225 421 arkllevvenvrrviaiEllaaaqglefrkaektaaelekvyeavRevveeleeDRvlapDleavkelle 490
                                              arkl +++en++++++iEllaaaqg+++r+++kt+++l+kv++avR+ v+++e D ++apD++av++l++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555 421 ARKLGDIAENTANILSIELLAAAQGVDLRAPHKTSPSLQKVMDAVRKDVAHYELDHYFAPDIAAVTRLVQ 490
                                              ********************************************************************** PP

                                TIGR01225 491 kesleaa 497
                                              ++++++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS07555 491 DGTIAKL 497
                                              *998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (506 nodes)
Target sequences:                          1  (506 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.67
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources